Impact of Pre-analytical Factors on the Success of Comprehensive Genomic Profiling in Gastrointestinal Tract Cancers

Impact of Pre-analytical Factors on the Success of Comprehensive Genomic Profiling in Gastrointestinal Tract Cancers | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Impact of Pre-analytical Factors on the Success of Comprehensive Genomic Profiling in Gastrointestinal Tract Cancers Takuma Iwata, Nobumi Suzuki, Gota Fujisawa, Yu Miyakawa, Kenji Tamada, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7344606/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Purpose Comprehensive genomic profiling (CGP) is an essential tool in precision oncology, but CGP success can be influenced by pre-analytical factors. This study aimed to evaluate the impact of pre-analytical factors on CGP success using formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with gastrointestinal (GI) tract cancers. Methods We retrospectively analyzed 226 FFPE tissue samples from patients with GI tract cancers at our institution between June 2020 and July 2025. Sampling methods were categorized as endoscopic biopsy, primary surgery, or metastatic surgery. The associations between CGP success and pre-analytical factors were assessed using multivariate analysis. Results Endoscopic biopsy samples had a significantly lower success rate than the primary and metastatic surgery samples ( p = 0.0001). Prolonged FFPE storage was independently associated with reduced CGP success ( p < 0.0001). Logistic regression analysis demonstrated that the probability of CGP success decreased sharply with longer FFPE storage for endoscopic biopsy samples, falling to 50% at approximately 1.4 years, whereas surgical samples maintained over 50% success for more than 4 years. Primary tumor site ( p = 0.144), prior chemotherapy ( p = 0.855), and sample collection institution ( p = 0.778) were not significantly associated with CGP success. Conclusion Sampling method and FFPE storage duration were critical determinants of CGP success in GI tract cancers. Endoscopic biopsy samples were more susceptible to degradation than surgical resection samples, highlighting the need for optimal pre-analytical handling and timely submission to maximize the clinical utility of CGP. Gastrointestinal cancers Comprehensive genomic profiling Endoscopic biopsy Pre-analytical factors Formalin-fixed paraffin-embedded Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7344606","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":502223046,"identity":"f8051529-6d05-437a-8938-d1959a0d3839","order_by":0,"name":"Takuma Iwata","email":"","orcid":"","institution":"The University of Tokyo","correspondingAuthor":false,"prefix":"","firstName":"Takuma","middleName":"","lastName":"Iwata","suffix":""},{"id":502223047,"identity":"30cc4bce-45fd-4e72-973d-4accad3192c9","order_by":1,"name":"Nobumi 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Tokyo","correspondingAuthor":false,"prefix":"","firstName":"Katsutoshi","middleName":"","lastName":"Oda","suffix":""},{"id":502223075,"identity":"488246e2-fd40-42da-b97f-0e858728c7c7","order_by":15,"name":"Narikazu Boku","email":"","orcid":"","institution":"IMSUT Hospital, The University of Tokyo","correspondingAuthor":false,"prefix":"","firstName":"Narikazu","middleName":"","lastName":"Boku","suffix":""},{"id":502223076,"identity":"c19a1736-ce7b-48c2-a56b-514e7ff8d6bf","order_by":16,"name":"Mitsuhiro Fujishiro","email":"","orcid":"","institution":"The University of Tokyo","correspondingAuthor":false,"prefix":"","firstName":"Mitsuhiro","middleName":"","lastName":"Fujishiro","suffix":""}],"badges":[],"createdAt":"2025-08-11 09:23:18","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7344606/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7344606/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":95802295,"identity":"103db9b8-122a-456f-8198-6e0aaf1b6d69","added_by":"auto","created_at":"2025-11-13 08:27:23","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1102738,"visible":true,"origin":"","legend":"","description":"","filename":"CGPOriginalArticleDDSFigureTableSupplement.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7344606/v1_covered_2a83db80-fd31-4150-9ba9-5341e371ab8d.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Impact of Pre-analytical Factors on the Success of Comprehensive Genomic Profiling in Gastrointestinal Tract Cancers","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Gastrointestinal cancers, Comprehensive genomic profiling, Endoscopic biopsy, Pre-analytical factors, Formalin-fixed paraffin-embedded","lastPublishedDoi":"10.21203/rs.3.rs-7344606/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7344606/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003ePurpose\u003c/h2\u003e\u003cp\u003eComprehensive genomic profiling (CGP) is an essential tool in precision oncology, but CGP success can be influenced by pre-analytical factors. This study aimed to evaluate the impact of pre-analytical factors on CGP success using formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with gastrointestinal (GI) tract cancers.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e\u003cp\u003eWe retrospectively analyzed 226 FFPE tissue samples from patients with GI tract cancers at our institution between June 2020 and July 2025. Sampling methods were categorized as endoscopic biopsy, primary surgery, or metastatic surgery. The associations between CGP success and pre-analytical factors were assessed using multivariate analysis.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eEndoscopic biopsy samples had a significantly lower success rate than the primary and metastatic surgery samples (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.0001). Prolonged FFPE storage was independently associated with reduced CGP success (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.0001). Logistic regression analysis demonstrated that the probability of CGP success decreased sharply with longer FFPE storage for endoscopic biopsy samples, falling to 50% at approximately 1.4 years, whereas surgical samples maintained over 50% success for more than 4 years. Primary tumor site (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.144), prior chemotherapy (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.855), and sample collection institution (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.778) were not significantly associated with CGP success.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e\u003cp\u003eSampling method and FFPE storage duration were critical determinants of CGP success in GI tract cancers. Endoscopic biopsy samples were more susceptible to degradation than surgical resection samples, highlighting the need for optimal pre-analytical handling and timely submission to maximize the clinical utility of CGP.\u003c/p\u003e","manuscriptTitle":"Impact of Pre-analytical Factors on the Success of Comprehensive Genomic Profiling in Gastrointestinal Tract Cancers","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-21 09:33:48","doi":"10.21203/rs.3.rs-7344606/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"f4486dea-ed44-46e9-9428-2943bbfc02d9","owner":[],"postedDate":"August 21st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-11-12T20:53:17+00:00","versionOfRecord":[],"versionCreatedAt":"2025-08-21 09:33:48","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7344606","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7344606","identity":"rs-7344606","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}